Abstract
RAPD analysis was applied to onion (Allium cepa) and otherAllium species in order to assess the degree of polymorphism within the genus and to investigate if this approach was suitable for genetic studies of onion. Seven cultivars ofA. cepa, including shallot, and single cultivars of Japanese bunching onion (A. fistulosum), chive (A. schoenoprasum), leek (A. ampeloprasum), and a wild relative of onion (A. roylei), were evaluated for variability using a set of 20 random 10-mer primers. Seven out of the twenty primers revealed scorable polymorphisms between cultivars ofA. cepa and these will be further evaluated for use in genetic mapping. Wide variations in banding profiles between species were observed with nearly every primer tested. These were assessed for use in systematic studies within the genus. Ninety-one band positions were scored (+/-) for all the cultivars studied. Genetic distances between each of the cultivars were calculated and cluster analysis was used to generate a dendrogram showing phylogenetic relationships between them. The resulting analysis was in broad agreement with previous classifications of the species studied, confirming the validity of the method. However, amongst the species studied, it placedA. roylei as the closest relative ofA. cepa, questioning the current classification of the former species in the section Rhizideum.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bennett MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Phil Trans R Soc Lond B274:227–274
Caetano-Anolles, Bassam BJ, Gresshoff PM (1991) DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Biotechnology 9:553–556
Carlson JE, Tulsieram LK, Glaubitz JC, Luk VWK, Kauffeldt C, Rutledge R (1991) Segregation of random amplified DNA markers in F1 progeny of conifers. Theor Appl Genet 83:194–200
Church GM, Gilbert W (1984) Genomic sequencing. Proc Natl Acad Sci USA 81:1991–1995
Cryder CM, Corgan JN, Urquhart NS, Clason D (1991) Isozyme analysis of progeny derived from (Allium fistulosum xAllium cepa) xAllium cepa. Theor Appl Genet 82:337–345
Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21
Feinberg AP, Vogelstein B (1983) A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132:6–13
Feinberg AP, Vogelstein B (1984) Addendum: a technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 137:226–227
Haiward T, Stalker T, LaRue E, Kochert G (1992) Use of singleprimer DNA amplifications in genetic studies of peanut (Arachis hypogaea L.). Plant Mol Biol 18:315–325
Hanelt P (1990) (Allium) Taxonomy, evolution and history. In: Rabinowitch HD, Brewster JL (eds) Onions and allied crops vol 1. Botany, physiology and genetics. CRC Press Inc, Boca Raton, Florida, pp 1–26
Havey MJ (1991) Phylogenetic relationships among cultivatedAllium species from restriction enzyme analysis of the chloroplast genome. Theor Appl Genet 81:752–757
Helentjaris T, Slocum M, Wright S, Schaeffer A, Nienhuis J (1986) Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphism. Theor Appl Genet 72:761–769
Henfrey RD, Slater RJ (1988) Isolation of plant nuclei. In: Walker JM (ed) Methods in Molecular Biology, vol 4. Humana Press, New Jersey, pp 447–452
Klein-Lankhorst RM, Vermunt A, Weide R, Liharska T, Zabel P (1991) Isolation of molecular markers for tomato (Lycopersicon esculentum) using random amplified polymorphic DNA (RAPD). Theor Apply Genet 83:108–114
Kochert G, Halward T, Branch WD, Simpson CE (1991) RFLP variability in peanut (Arachis hypogaea L.) cultivars and wild species. Theor Appl Genet 81:565–570
Manly BFJ (1986) Multivariate statistical analysis: a primer. Chapman and Hall, London, pp 100–113
Martin GB, Williams JGK, Tanksley SD (1991) Rapid identification of markers linked to aPseudomonas resistance gene in tomato by using random primers and near isogenic lines. Proc Natl Acad Sci USA 88:2336–2340
McCollum GD (1976) Onions and allies. In: Simmonds NW (ed) Evolution of crop plants. Longman, London, pp 186–190
Melchinger AE, Boppenmaier J, Dhillon BS, Pollmer WG, Herrmann RG (1992) Genetic diversity for RFLPs in European maize inbreds. II. Relation to performance of hybrids within versus between heterotic groups for forage traits. Theor Appl Genet 84:672–681
Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583
Peffley EB, Mangum PD (1990) Introgression ofA. fistulosum L. intoA. cepa L.: cytogenetic evidence. Theor Appl Genet 79:113–118
Peffley EB, Currah L (1988) The chromosomal locations of enzyme coding genes Adh-1 and Pgm-1 inA. fistulosum L. Theor Appl Genet 75:945–949
Peffley EB, Corgan JN, Horak KE, Tanksley SD (1985) Electrophoretic analysis ofAllium alien addition lines. Theor Appl Genet 71:176–184
Rafalski JA, Tingey SV, Williams JGK (1991) RAPD markers ⊕ new technology for genetic mapping and plant breeding. Ag Biotech News Info 3:645–648
Reiter RS, Williams JGK Feldmann KA, Rafalski JA, Tingey SV, Scolnik PA (1992) Global and local genome mapping inArabidopsis thaliana by using recombinant inbred lines and RAPDs. Proc Natl Acad Sci USA 89:1477–1481
Riocroch A, Peffley EB, Baker RJ (1992) Chromosomal location of rDNA inAllium: in situ hybridisation using biotinand fluorescein-labelled probes. Theor Appl Genet 83:413–418
Rogers JS (1972) Measures of genetic similarity and genetic distance. Studies in genetics VII. Univ Texas Publ 7213:145–153.
Ruano G, Brash DE, Kidd KK (1991) PCR: the first few cycles. Amplifications 7:1–4
Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer length polymorphisms in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014–8018
Sambrook J, Fritsch EF, Maniatis J (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp 1.43–1.46
Tanksley SD, Miller J, Paterson A, Bernatzky R (1987) Molecular mapping of plant chromosomes. In: Gustafson JP, Appels R (eds) Chromosome structure and function. Plenum Press, New York, pp 157–173
Traub H (1968) The subgenera, sections and subsections ofAllium L. Plant Life 24:147–163
Valk P van der, de Vries SE, Everink JT, Verstappen F, de Vries JN (1991) Preand post-fertilisation barriers to backcrossing the interspecific hybrid betweenAllium fistulosum L. andA. cepa L. withA. cepa. Euphytica 53:201–209
Vvedensky A (1944) The genusAllium in the USSR. Herbertia 11:65–218
Wang ZY, Second G, Tanksley SD (1992) Polymorphism and phylogenetic relationships among species in the genusOryza as determined by analysis of nuclear RFLPs. Theor Appl Genet 83:565–581
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535
Author information
Authors and Affiliations
Additional information
Communicated by J W. Snape
Rights and permissions
About this article
Cite this article
Wilkie, S.E., Isaac, P.G. & Slater, R.J. Random amplified polymorphic DNA (RAPD) markers for genetic analysis inAllium . Theoret. Appl. Genetics 86, 497–504 (1993). https://doi.org/10.1007/BF00838566
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00838566